Erica VanHoosen

Summer Bioinformatics Abstract

The work completed during the summer bioinformatics internship was two-fold. The first half of the internship consisted mainly of lab work in Dr. Dan Wall’s lab studying Myxococcus xanthus. Antibiotic TA (myxovirescin) is a secondary metabolite produced by M. xanthus that is hypothesized to play some role in predation. Two different types of experiments were completed in order to try and determine this antibiotic’s role, a predation experiment as well as a zone-of-inhibition experiment. In these experiments several different Gram-negative and Gram-positive prey organisms were tested against both the wild type M. xanthus strain and a TA- mutant strain that is unable to produce the TA antibiotic. It was observed that antibiotic TA was only effective on some of the prey organisms but not others. There was no visible pattern of the type of organisms that it was most effective against (i.e. Gram-negative, below a certain size etc.) Similar to other antibiotics, antibiotic TA appears to be prey dependent. Several more experiments need to be completed to make any further conclusions.

During the second half of the internship the focus was put more on bioinformatics by looking at the TA gene from a phylogenetic standpoint. There are several domains that make up the TA gene cluster but the Ketoacyl-N terminus and Ketoacyl-C terminus domains (known collectively as the KS domain) which always occur together in M. xanthus were chosen as the focus of this analysis. The amino acid sequence of the KS domain was blasted against 10 other bacterial species, of varying relatedness to M. xanthus, that also contain this domain. A tree was produced using both RaXml and Mr. Bayes (still unfinished) using the model WAG+I+G and the trees were then analyzed. It was observed that the PKS 1 proteins (containing 3 or more repeats of the KS domain sequence) and the PKS 2 proteins (containing 2 or less repeats) were obviously separated into different clades of the tree with few exceptions. The higher ordered proteins (5, 6 and 7 repeats) also seemed, more or less, to follow each other through the branches of the tree. Although somewhat unrelated, there was also a very large section of Streptomyces griseus duplications that was actually the most striking part of the tree.